Job ID = 6498449 SRX = SRX511347 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:04:26 prefetch.2.10.7: 1) Downloading 'SRR1217609'... 2020-06-26T00:04:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:06:57 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:06:57 prefetch.2.10.7: 1) 'SRR1217609' was downloaded successfully Read 12953076 spots for SRR1217609/SRR1217609.sra Written 12953076 spots for SRR1217609/SRR1217609.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:29 12953076 reads; of these: 12953076 (100.00%) were paired; of these: 1527863 (11.80%) aligned concordantly 0 times 10344474 (79.86%) aligned concordantly exactly 1 time 1080739 (8.34%) aligned concordantly >1 times ---- 1527863 pairs aligned concordantly 0 times; of these: 12654 (0.83%) aligned discordantly 1 time ---- 1515209 pairs aligned 0 times concordantly or discordantly; of these: 3030418 mates make up the pairs; of these: 2567548 (84.73%) aligned 0 times 389668 (12.86%) aligned exactly 1 time 73202 (2.42%) aligned >1 times 90.09% overall alignment rate Time searching: 00:12:29 Overall time: 00:12:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2369770 / 11433871 = 0.2073 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:26:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 09:26:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:36: 1000000 INFO @ Fri, 26 Jun 2020 09:26:41: 2000000 INFO @ Fri, 26 Jun 2020 09:26:47: 3000000 INFO @ Fri, 26 Jun 2020 09:26:52: 4000000 INFO @ Fri, 26 Jun 2020 09:26:57: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:27:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 09:27:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:27:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:27:03: 6000000 INFO @ Fri, 26 Jun 2020 09:27:07: 1000000 INFO @ Fri, 26 Jun 2020 09:27:08: 7000000 INFO @ Fri, 26 Jun 2020 09:27:13: 2000000 INFO @ Fri, 26 Jun 2020 09:27:14: 8000000 INFO @ Fri, 26 Jun 2020 09:27:18: 3000000 INFO @ Fri, 26 Jun 2020 09:27:20: 9000000 INFO @ Fri, 26 Jun 2020 09:27:24: 4000000 INFO @ Fri, 26 Jun 2020 09:27:26: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:27:30: 5000000 INFO @ Fri, 26 Jun 2020 09:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 09:27:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:27:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:27:31: 11000000 INFO @ Fri, 26 Jun 2020 09:27:36: 6000000 INFO @ Fri, 26 Jun 2020 09:27:37: 1000000 INFO @ Fri, 26 Jun 2020 09:27:37: 12000000 INFO @ Fri, 26 Jun 2020 09:27:42: 7000000 INFO @ Fri, 26 Jun 2020 09:27:42: 2000000 INFO @ Fri, 26 Jun 2020 09:27:43: 13000000 INFO @ Fri, 26 Jun 2020 09:27:47: 8000000 INFO @ Fri, 26 Jun 2020 09:27:48: 3000000 INFO @ Fri, 26 Jun 2020 09:27:49: 14000000 INFO @ Fri, 26 Jun 2020 09:27:53: 9000000 INFO @ Fri, 26 Jun 2020 09:27:54: 4000000 INFO @ Fri, 26 Jun 2020 09:27:55: 15000000 INFO @ Fri, 26 Jun 2020 09:27:59: 10000000 INFO @ Fri, 26 Jun 2020 09:28:00: 5000000 INFO @ Fri, 26 Jun 2020 09:28:00: 16000000 INFO @ Fri, 26 Jun 2020 09:28:05: 11000000 INFO @ Fri, 26 Jun 2020 09:28:06: 6000000 INFO @ Fri, 26 Jun 2020 09:28:06: 17000000 INFO @ Fri, 26 Jun 2020 09:28:11: 12000000 INFO @ Fri, 26 Jun 2020 09:28:11: 7000000 INFO @ Fri, 26 Jun 2020 09:28:12: 18000000 INFO @ Fri, 26 Jun 2020 09:28:15: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:28:15: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:28:15: #1 total tags in treatment: 9057043 INFO @ Fri, 26 Jun 2020 09:28:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:28:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:28:16: #1 tags after filtering in treatment: 4877682 INFO @ Fri, 26 Jun 2020 09:28:16: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 26 Jun 2020 09:28:16: #1 finished! INFO @ Fri, 26 Jun 2020 09:28:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:28:16: #2 number of paired peaks: 7252 INFO @ Fri, 26 Jun 2020 09:28:16: start model_add_line... INFO @ Fri, 26 Jun 2020 09:28:16: start X-correlation... INFO @ Fri, 26 Jun 2020 09:28:16: end of X-cor INFO @ Fri, 26 Jun 2020 09:28:16: #2 finished! INFO @ Fri, 26 Jun 2020 09:28:16: #2 predicted fragment length is 148 bps INFO @ Fri, 26 Jun 2020 09:28:16: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 26 Jun 2020 09:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.05_model.r INFO @ Fri, 26 Jun 2020 09:28:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:28:16: 13000000 INFO @ Fri, 26 Jun 2020 09:28:17: 8000000 INFO @ Fri, 26 Jun 2020 09:28:22: 14000000 INFO @ Fri, 26 Jun 2020 09:28:23: 9000000 INFO @ Fri, 26 Jun 2020 09:28:28: 15000000 INFO @ Fri, 26 Jun 2020 09:28:29: 10000000 INFO @ Fri, 26 Jun 2020 09:28:29: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:28:34: 16000000 INFO @ Fri, 26 Jun 2020 09:28:35: 11000000 INFO @ Fri, 26 Jun 2020 09:28:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:28:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:28:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.05_summits.bed INFO @ Fri, 26 Jun 2020 09:28:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10905 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:28:40: 17000000 INFO @ Fri, 26 Jun 2020 09:28:40: 12000000 INFO @ Fri, 26 Jun 2020 09:28:45: 18000000 INFO @ Fri, 26 Jun 2020 09:28:46: 13000000 INFO @ Fri, 26 Jun 2020 09:28:49: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:28:49: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:28:49: #1 total tags in treatment: 9057043 INFO @ Fri, 26 Jun 2020 09:28:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:28:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:28:49: #1 tags after filtering in treatment: 4877682 INFO @ Fri, 26 Jun 2020 09:28:49: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 26 Jun 2020 09:28:49: #1 finished! INFO @ Fri, 26 Jun 2020 09:28:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:28:50: #2 number of paired peaks: 7252 INFO @ Fri, 26 Jun 2020 09:28:50: start model_add_line... INFO @ Fri, 26 Jun 2020 09:28:50: start X-correlation... INFO @ Fri, 26 Jun 2020 09:28:50: end of X-cor INFO @ Fri, 26 Jun 2020 09:28:50: #2 finished! INFO @ Fri, 26 Jun 2020 09:28:50: #2 predicted fragment length is 148 bps INFO @ Fri, 26 Jun 2020 09:28:50: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 26 Jun 2020 09:28:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.10_model.r INFO @ Fri, 26 Jun 2020 09:28:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:28:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:28:52: 14000000 INFO @ Fri, 26 Jun 2020 09:28:57: 15000000 INFO @ Fri, 26 Jun 2020 09:29:02: 16000000 INFO @ Fri, 26 Jun 2020 09:29:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:29:07: 17000000 INFO @ Fri, 26 Jun 2020 09:29:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:29:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:29:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.10_summits.bed INFO @ Fri, 26 Jun 2020 09:29:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9272 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:29:13: 18000000 INFO @ Fri, 26 Jun 2020 09:29:16: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:29:16: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:29:16: #1 total tags in treatment: 9057043 INFO @ Fri, 26 Jun 2020 09:29:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:29:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:29:16: #1 tags after filtering in treatment: 4877682 INFO @ Fri, 26 Jun 2020 09:29:16: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 26 Jun 2020 09:29:16: #1 finished! INFO @ Fri, 26 Jun 2020 09:29:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:29:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:29:17: #2 number of paired peaks: 7252 INFO @ Fri, 26 Jun 2020 09:29:17: start model_add_line... INFO @ Fri, 26 Jun 2020 09:29:17: start X-correlation... INFO @ Fri, 26 Jun 2020 09:29:17: end of X-cor INFO @ Fri, 26 Jun 2020 09:29:17: #2 finished! INFO @ Fri, 26 Jun 2020 09:29:17: #2 predicted fragment length is 148 bps INFO @ Fri, 26 Jun 2020 09:29:17: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 26 Jun 2020 09:29:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.20_model.r INFO @ Fri, 26 Jun 2020 09:29:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:29:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:29:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:29:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:29:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:29:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511347/SRX511347.20_summits.bed INFO @ Fri, 26 Jun 2020 09:29:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7466 records, 4 fields): 10 millis CompletedMACS2peakCalling